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He said the US government had a “pretty good idea” who was responsible but did not elaborate.

Many cyber-attacks in the past have been blamed on China or Russia, and one of the Pentagon’s fears is that eventually a terrorist group will acquire the ability to steal data.

Mr Lynn disclosed the March attack in a speech outlining a new cyber-strategy, which formally declares cyberspace a new warfare domain, much like air, land and sea.

It calls for developing more resilient computer networks so the military can continue to operate if critical systems are breached or taken down

The Pentagon has long worried about the vulnerability of its computer systems. Its concern has grown as the military becomes more dependent, not only on its own computers, but also on those of its contractors including providers of fuel and electricity.

Mr Lynn said intrusions in the last few years had compromised some of the Pentagon’s most sensitive systems, including surveillance technologies and satellite communications systems.

Penetrations of defence industry computer networks have targeted a wide swath of military hardware, including missile tracking systems and drone aircraft.

At his Senate confirmation hearing last month the new defence secretary Leon Panetta said there was a “strong likelihood that the next Pearl Harbor”could be a cyber-attack that cripples the US power grid, and financial and government systems.

Marine General James Cartwright, the vice chairman of the Joint Chiefs of Staff, said the US should focus more on offensive, rather than defensive, cyber measures.

He said: “For the Department of Defence, our networks are really our lifeblood. If it’s OK to attack me and I’m not going to do anything other than improve my defences every time you attack me, it’s difficult.”

Earlier this year, President Barack Obama signed executive orders laying out how far military commanders around the globe can go in using cyber-attacks and other computer-based operations against enemies.

SourceTelegraph News